The gene in question is on the antisense strand. Thus,
compared to the search string, the gene runs in the reverse
direction and the short protein produced by clone #2 should
have nothing to do with the full-length sensor histidine kinase
protein (the alignment of the two sets of codons are also
off by one nucleotide). However, the short RNA produced
during the transcription of clone #2 will have strong affinity
for the double-stranded DNA within this portion of the gene,
potentially affecting its regulation.

When expanding the search to include a list of
representative genomes curated by NCBI, portions of this
clone can be seen in diverse organisms. The first search
brought up hits from 30 different bacterial and one fungal
species. This was reduced to high-scoring hits only, from
four bacterial species, by changing the Expect Threshold
and Word Size (figure 4). Interestingly, these results did not
overlap with those from a search of E. coli specifically, nor
was E. coli in these search results. This indicates that short,
random search strings have a high probability of aligning
with known DNA sequences.

BLAST results for the remaining clones compared to
E. coli are summarized in table 2. BLAST comparisons
for the seven assay clones compared to a curated list of
representative genomes are given in table 3.

Among the multiple random test sequences I generated
that had not been filtered for activity in E. coli, no significant
matches with the E. coli genome were found. But, as in the
other tests, short sections of 20–30 nucleotides had significant
matches to a range of other organisms (figure 5 and table 4).

Discussion

Though the sequences Neme et al. tested were randomized,
intelligently designed sequences were placed on both sides
of each random sequence to facilitate its integration into the
bacterial genome. Our concept of what a gene is has changed
dramatically over the past few decades. The ‘one gene, one
enzyme’ mantra is a thing of the past. The modern definition
of a gene includes alternative splicing variants of the protein
for which the gene codes, 16 as well as the regulatory regions,
which may include enhancer regions far away from the gene
itself. Evolutionists generally try to downplay the idea of
functional information in biology. This does not mean that
biblical creationists have not mishandled the subject over
time, 17 but the information content in living things is a subject
evolutionists invariably avoid. Neme et al. did exactly that,
and this led to fatal mistakes in their analysis.

Most of the clones examined received highly significant
matches to the E. coli genome using BLASTn. However,
the matching sections were all small ( 18–43 nucleotides).
Percent identity ranged up to 100% over those small sections,
meaning that the authors unknowingly identified real portions
of real genes. The diversity of organisms represented in
these matches was surprising. A few microorganisms, at
best, other than E. coli were expected on the list, yet species
that received significant hits ranged from beaver to bacilli
(table 1). The fact that 20–40 nucleotide sections of different
genomes were highlighted indicates their experimental setup
was sufficient to explore a considerable portion of gene space
in that size range.

< 40

1 30 60 90 120 150

> = 200 40-50 50-80

Colour key for alignment scores

Query

80-200

Figure 4. Graphical results for a BLAST search comparing clone 2 against
a curated set of representative genomes. In order to increase specificity
and reduce the number of hits, the Expect Threshold was set at 10 and
the Word Size at 15. Eight diverse bacterial genomes are represented
here, including representatives from genera Steptomyces, Lysobacter,
Blastococcus, Dietzia, Geodermatophilus, and Cupriavidus.

Figure 3. Details of the 27-bp region highlighted in figure 1, showing 89%
identity at the nucleotide level. ‘Query’ is the test sequence (clone #2).
The match was generated for nucleotides 80–106 (out of 150) in the test
sequence against the ‘Subject’ E. coli genome (strain 5CRE51).

Figure 2. Graphical results for a BLAST search comparing clone #2 (the
first clone in the database) against E. coli. The genomes of multiple E. coli
strains are in the NCBI database, hence the multiple identical hits. This
small 27-bp segment is part of the sensor histidine kinase gene that is
involved in citrate metabolism.

Colour key for alignment scores

Query

< 40 > = 200 40-50 50-80 80-200

1 300 600 900 120 1500

Figure 5. BLAS T results generated by comparing a long string of random
nucleotides to the entire nucleotide collection at NCBI. The lengths
and percent matches of the flagged sections are similar to the others
discovered above.